Kolář lab at UCT Prague

Reaction Path Averaging

published 2017-02-13

The DNA is one of the best-known biomolecules. Upon electromagnetic radiation, an electron may be released from a nucleobase, resulting in a positive electron hole. The hole may travel across the nucleobases turning the DNA into a sort of nanowire. This is a rather established fact. The shape of the DNA is so classic that it is natural to ask how the DNA distorts upon the electron transfer. With Tom Kubař we've recently attempted to answer. We used a computational approach, which we called Reaction Path Averaging (RPA).

Reaction Path Averaging

Text about Biophysics in Vesmír

published 2017-02-11

In October 2016, Klaus Schulten passed away. He was a professor at the University of Illinois, USA, and a pioneer of computer simulations in biophysics. I've met him just once, but that episode left strong memories. In a recent article for Vesmír, I put Klaus' life into context with the progress in computational biophysics. Written in Czech, available for subscribers.

HTML5 in Bratislava

published 2016-12-09

Michal Pitonak invited me to Bratislava to give a talk on sigma-holes. The Department of physical and theoretical chemistry at the Comenius University in Bratislava is world-renowned for the accurate quantum chemical calculations. They develop, benchmark and apply perhaps the highest quantum chemistry one can imagine.

Ribosome Meeting in Heidelberg

published 2016-11-25

Last week, I attended a meeting on ribosomes. All the german experts on all aspects of ribosome research at one place. I gave a talk on the simulations I'm trying to establish. Given that there were like only two more simulation guys in the audience, the feedback that I got was in general quite positive.

Ribosome meeting in Heidelberg

This is what I saw in the morning from the hotel window, after a dreamless night of rendering the last videos for my talk.

CPU-Time Granted

published 2016-10-28

Our computational proposal with Helmut and others has just been approved! We will receive 67 million core-hours to study RNA-protein interactions within a prokaryotic ribosome. Thanks to the Leibniz Rechnenzentrum in Munich, Germany, our simulations of more than 2 million atoms will not take ages and I'll bring some news soon, hopefully.

Ribosomal exit tunnel

The figure shows the tRNA at the catalytic center of the ribosome (yellow), the exit tunnel for newly synthesized proteins (gray surface), and two ribosomal proteins (red and blue). The lines with dots are chemical bonds between atoms, just to put it all into context.

Highly Cited Paper

published 2016-10-21

Good news! In June 2016, our review on sigma-hole calculations was ranked by Thomson Reuters Web of Science in the top 1 % of the academic field of chemistry. No matter that the paper has received 10 citations so far...

Highly cited paper

German Biophysical Society Meeting

published 2016-10-10

For the first time, I visited Erlangen. I presented a poster on DNA relaxation, which I recycled from the Hünfeld workshop. Hard to say if this was the reason why it attracted much less attention than before. There was a special session on electron and proton transfer, but I got the impression that the conference was biased towards lipids and their aggregates. For instance, there were very few contributions on the intrinsically disordered proteins, which was - as far as I've heard - one of the hottest topics on the American Biophysical Society Meeting...

Poster on the Reaction Path Averaging

I will definitely remember the talk of Peter Tieleman about lipid localization in membranes studied by coarse-grained simulations. For me, his talk was the example of how not to present a plenary talk if you are the leader in the field. Some of the (positive) reactions afterwards only showed that people tend to believe data more if presented by a "big name."

Relay Run 2017

As a second runner, I took part in a relay run during Sommerfest of the Max Planck Institute for Biophysical Chemistry. 11 am, 30 °C, 5 minutes full steam. Thanks the team.

published 2016-06-22

Poster in Hünfeld

published 2016-06-04

Workshop on Computer Simulations and Theory of Biomolecules in Hünfeld is a pretty traditional event (runs since 2001). I've been there already for a couple of times, but this year I took part as a member of the organizing Department from Göttingen. As usual, the two days were fairly relaxed. The talks are given only by students and postdocs, people know each other from before and spent much time discussing science. I contributed with a poster on DNA relaxation. Shake it off, DNA!

Reaction Path Averaging: Poster

"h is an abbreviation for huhohshdhjha"

qstat -help (SGE)

published 2016-05-22